"There are other executives who remain unnamed at other companies who would be tempted to go for every last candy in the dish," he said.
Apple also gave pay increases to several senior executives.
Chief financial officer Peter Oppenheimer's package was worth US$68.6 million, up from US$1.42 million last year.
Like Cook, his pay packet was boosted by stock awards; his were valued at US$66.2 million.
The senior vice-president of technologies, Bob Mansfield, received US$85.5 million, including US$83.1 million in stock.
Cook reportedly asked Mansfield, who was formerly in charge of hardware engineering, to come out of retirement amid a management shake- up this year.
Mansfield's stock options were vesting more quickly than those of other executives, said Foley.
"He was threatening to retire and from a bench strength, leadership viewpoint, they decided they couldn't afford to have him leave."
The senior vice-president of operations, Jeff Williams, who manages Apple's supply chain, received US$68.7 million.
The company's general counsel, Bruce Sewell, who has managed Apple's patent litigation, received US$69 million, compared with US$1.41 million last year.
Cook's base salary last year was $900,000. His total compensation then put him ahead of the highest-paid chief executives at the time, according to Equilar Inc, which tracks executive pay.
Oracle chief executive Larry Ellison received US$77.6 million last year; at Microsoft, Steve Ballmer's pay package was worth US$1.38 million.
Amazon.com paid chief executive Jeffrey Bezos a salary of US$81,840 last year and no stock awards, making him the lowest paid among large technology companies.
Cook faced a setback this year over problems with Apple's map application which forced the company to let Google's map app back on to iPads and iPhones.
The company's stock price has fallen 27 per cent from a September 19 record high, and was at US$515.06 in New York yesterday.
Even with the decline since September, the stock is up 27 per cent for this year.
But at least five analysts have cut their price targets for Apple since December 16, some saying Apple's iPhone and iPad sales may not meet projections.
The reports from Citigroup Inc, Pacific Crest Securities, Mizuho Securities USA, BMO Capital Markets and Canaccord Genuity are a reversal from earlier this year, when analysts were more upbeat, at least two saying Apple shares would top US$1000.